The manifesto concludes with, "The RYM must also lead to the effective organization needed to survive and to create another battlefield of the revolution. A revolution is a war; when the Movement in this country can defend itself militarily against total repression it will be part of the revolutionary war. This will require a cadre organization, effective secrecy, self-reliance among the cadres...".[11] The manifesto also asserted that African-Americans were a "black colony" within a U.S. government that was doomed to overextend itself. And the RYM was needed to quicken this process. Dohrn said, "The best thing that we can be doing for ourselves, as well as for the [Black] Panthers and the revolutionary black liberation struggle, is to build a fucking white revolutionary movement."[10]

The ninth annual national SDS conference was held at the Chicago Coliseum on June 18–22, 1969, and the SDS collapsed in a Revolutionary Youth Movement-led upheaval. Soon after the Revolutionary Youth Movement became known as the Weatherman. Dohrn led the Weatherman faction in the SDS fight and continued to be a leader afterward.[12][13]Larry Grathwohl, an FBI informant who was with the Weatherman from autumn 1969 through spring 1970, considered her one of the two top leaders of the organization, along with Bill Ayers.[14] On May 26, 1968, as a speaker for the National Lawyers Guild, Dohrn said she was filing a motion in federal court asking for an injunction to halt any disciplinary action that was being taken against student activists and represented students from Columbia University who were striking and protesting. On June 14, 1968, Dohrn was elected the Inter-organizational Secretary of SDS, and, once elected, was asked if she was a socialist. She replied, "I consider myself a revolutionary communist."[15] From August 30 to September 1, 1968, Dohrn visited Yugoslavia. Her involvement with SDS and political advocacy stretch beyond the United States as well, as she and other SDS leaders had met with representatives from North Vietnam and the National Liberation Front of South Vietnam in Budapest, Hungary to discuss peace talks. She and a delegation from the SDS also traveled to Cuba via Mexico City, Mexico on July 4, 1969, and later arrived in Canada via a Cuban vessel on August 16, 1969.

On the night of October 1, 1968, Dohrn spoke at a meeting in Chicago to condemn Chicago's Mayor Daley's orders to attack protesters during the 1968 Democratic National Convention. Then, from October 11 to 13, she and SDS held a national meeting at the University of Colorado Boulder wherein Dohrn was a speaker addressing concerns about where the movement was headed and what involvement they could expect as governmental tensions mounted and the student movement splintered into factions. On October 11, 1968, Dohrn suggested she would expand the movement to non-students and do all that was necessary to complete the job of "attack, expose, destroy."[16] Dohrn continued to give speeches on behalf of SDS and Weather Underground and attend leadership conferences for both organizations. On January 29 and 30, 1969, in recognition of the tenth anniversary of the Cuban Revolution, the University of Washington held a Cuba teach-in where Dohrn was a speaker on campus. A month later at a press conference at the regional headquarters of SDS in Chicago, Dohrn spoke of the plans that were under way to "attack" college graduation ceremonies across the country, saying, "Our presence will be known at the graduation ceremonies where the big people will come as speakers." By that time, Dohrn was now known as a National Interim Committee member of the SDS and a member of the Weatherman group.

Dohrn was a principal signatory on the Weather Underground's "Declaration of a State of War" in May 1970 that formally declared "war" on the U.S. Government, and completed the group's transformation from political advocacy to violent action. She recorded the declaration and sent a transcript of a tape recording to the New York Times. Dohrn also co-wrote (with Bill Ayers) and published the subversive manifesto Prairie Fire in 1974, and participated in the covertly filmed Underground in 1976. In late 1975, the Weather Underground put out an issue of a magazine, Osawatamie, which carried an article by Dohrn titled, "Our Class Struggle", described as a speech given to the organization's cadres on September 2 of that year. In the article, Dohrn clearly stated support for communist ideology:[17]

We are building a communist organization to be part of the forces which build a revolutionary communist party to lead the working class to seize power and build socialism. [...] We must further the study of Marxism-Leninism within the WUO [Weather Underground Organization]. The struggle for Marxism-Leninism is the most significant development in our recent history. [...] We discovered thru our own experiences what revolutionaries all over the world have found — that Marxism-Leninism is the science of revolution, the revolutionary ideology of the working class, our guide to the struggle [...]

According to a 1974 FBI study of the group, Dohrn's article signaled a developing commitment to Marxism-Leninism that had not been clear in the group's previous statements, despite their trips to Cuba and contact with Vietnamese communists there.[17]

Dohrn was criticized for comments she reportedly made about the murders of actress Sharon Tate and retail store owners Leno and Rosemary LaBianca by the Charles Manson clan. In a speech during the December 1969 "War Council" meeting organized by the Weathermen, attended by about 400 people in Flint, Michigan, Dohrn said, "First they killed those pigs, then they ate dinner in the same room with them, then they even shoved a fork into the pig Tate's stomach! Wild!"[18][19][20] In greeting each other, delegates to the war council often spread their fingers to signify the fork.[10]

In 2008, Dohrn's husband, Bill Ayers, described the story as a "Big Lie" and said Dohrn's comments were taken out of context.[21]

On August 22, 1969, Dohrn was arrested in Chicago and charged with possession of drugs. The defense argued that Chicago Police had conducted an illegal search of the car in which she was a passenger, which led Judge Kenneth R. Wendt of the Narcotics Court of Chicago to dismiss the charges. On September 20, 1969, at an anti-Vietnam rally at the Davis Cup tennis tournament in Cleveland, police arrested Dohrn and twenty other persons on charges of disorderly conduct. On September 26, 1969, Dohrn was arrested again in Chicago during a rally in support of the eight men accused of conspiracy concerning the riot during the 1968 Democratic National Convention, who were being tried on riot conspiracy charges. Dohrn was next arrested on October 9, 1969, by the Chicago police during a rally for the women’s faction of the Weathermen group and was later released on a one thousand dollar bond.[22] On October 31, 1969, a grand juryindicted 22 people, including Dohrn, for their involvement with the trial of the Chicago Eight, and she was again indicted on April 2, 1970, when a Federal Grand Jury indicted twelve members of the Weatherman group on conspiracy charges in violation of anti-riot acts during the "Days of Rage."[16][23] However, all of these convictions were reversed on November 21, 1972, by the United States Court of Appeals for the Seventh Circuit on the basis the judge was biased in his refusal to permit defense attorneys to screen prospective jurors for cultural and racial bias.[24]

While on the run from police, Dohrn used many aliases (including Bernardine Rae Ohrnstein, H.T. Smith, and Marion Del Gado) and married another Weatherman leader, Bill Ayers, with whom she has two children. During the last years of their underground life, Dohrn and Ayers resided in Chicago, where they used the aliases Christine Louise Douglas and Anthony J. Lee.[1] In the late 1970s, the Weatherman group split into two factions, the "May 19 Coalition" and the "Prairie Fire Collective", with Dohrn and Ayers in the latter. The Prairie Fire Collective favored coming out of hiding, with members facing the criminal charges against them, while the May 19 Coalition remained in hiding. A decisive factor in Dohrn's coming out of hiding were her concerns about her children.[25]

From 1984 to 1988, Dohrn was employed by the prestigious Chicago law firm Sidley Austin,[29] where she was hired by Howard Trienens, the head of the firm at that time, who knew Thomas G. Ayers, Dohrn's father-in-law. "We often hire friends," Trienens told a reporter for the Chicago Tribune.[30] However, Dohrn had not been admitted to the New York or Illinois bar even though she had passed both bar exams, because she had not submitted an application to the New York Supreme Court's Committee on Character and Fitness.[29] Similarly, she was turned down by the Illinois ethics committee because of her criminal record. Trienens said of the Illinois rejection, "Dohrn didn't get a [law] license because she's stubborn. She wouldn't say she's sorry." [30]

In 1991, she was hired by Northwestern University School of Law, as an adjunct professor of law with the title "Clinical Associate Professor of Law". She was one of the founders of the Children and Family Justice Center, which supports the legal needs of adolescents and their families, in the Bluhm Legal Clinic at Northwestern Law. She left Northwestern Law on August 31, 2013. Because Dohrn was hired as an adjunct (a temporary assignment), her appointment did not need to be approved by the faculty. When law school officials were asked whether or not the dean hired Dohrn or the board of trustees approved the hiring, the school issued a statement in response stating: "While many would take issue with views Ms. Dohrn espoused during the 1960s, her career at the law school is an example of a person's ability to make a difference in the legal system."[30] Dohrn now serves on the board of numerous human rights committees. Since 2002, she has served as Visiting Law Faculty at the Vrije Universiteit in Amsterdam. Her legal work has focused on reforming the much criticized juvenile court system in Chicago and on advocating for human rights at the international level.

In 1994, Dohrn said of her political beliefs: "I still see myself as a radical."[31] On November 4, 2010, Dohrn was interviewed by Newsclick India. About the "Right" in the U.S., she said, "It's racist; it's armed; it’s hostile; it’s unspeakable." Referring to the Restoring Honor rally which was promoted by Glenn Beck and held on August 28, 2010, at the Lincoln Memorial in Washington, D.C., "You have white people armed, demanding the end to the [Obama] presidency." She also stated, "The real terrorist is the American government, state terrorism unleashed against the world."[32]

^Chepesiuk, Ron, "Sixties Radicals, Then and Now: Candid Conversations With Those Who Shaped the Era", McFarland & Company, Inc., Publishers: Jefferson, North Carolina, 1995, "Chapter 15: Bernardine Dohrn: From Revolutionary to Children's Rights Advocate", pages 223 and 224: "Dohrn, a leader of the Weather Underground" (p 223); "she then proceeded to lead the faction in the takeover of the organization's headquarters and the seizure of its assets"

^Grathwohl, Larry, and Frank, Reagan, Bringing Down America: An FBI Informant in with the Weathermen, Arlington House, 1977, page 110: "Ayers, along with Bernardine Dohrn, probably had the most authority within the Weatherman."

^Chepesiuk, Ron, "Sixties Radicals, Then and Now: Candid Conversations With Those Who Shaped the Era", McFarland & Company, Inc., Publishers: Jefferson, North Carolina, 1995, "Chapter 15: Bernardine Dohrn: From Revolutionary to Children's Rights Advocate", p 239;"Acknowledgements" section dated by the author as "Summer 1994" indicating interview took place before that